GitHub - rdpstaff/fungene_pipeline: Scripts and resources for analyzing sequence data for select eco-functional genes (original) (raw)

Functional Gene Pipeline Scripts

Intro...

Functional Gene Pipeline Scripts contains a set of python scripts that allows to run one or more individual tools offered by RDP FunGene Pipeline (http://fungene.cme.msu.edu). These tools are offered a modular fashion allowing researchers to choose the appropriate subset based on their needs.

Setup

Required Software

• RDPTools (https://github.com/rdpstaff/RDPTools)
• HMMER3 (http://hmmer.janelia.org protein aligner )
• Infernal 1.1 (http://infernal.janelia.org RRNA_16S_BACTERIA, RRNA_16S_ARCHAEA, RRNA_18S, RRNA_23S, and RRNA_28S rRNA Aligner)
• Note: The newest Infernal update changed the command for alignment to "-g --noprob"
• USEARCH (http://www.drive5.com/usearch chimera check)

Configuration

The path to the programs and resources are specfied in file config.ini. Modify the example config_skel.ini and rename it as config.ini.

Usage

The directory examplefiles contains the following files:

• sample 454 sequencing data file 1.TCA.454Reads.fastq in the 16S_seqdata folder. (Note: The pipeline_core.py no longer takes a file with the extension .qual as an argument. If this is an issue, please use a qual to fastq converter.)
• sample nifH nucleotide sequence files nifH_s1.fa and nifH_s2.fa.
• an example run descriptor file 16S_rundata.txt, a tab-delimited file containing a list of sample name, and forward and reverse primers for each barcode in each region. Note the header line must kept unchanged.
• an example gene option file gene_option.txt, specifies the parameters used for each program if different from the default. The section "[general]" specifies parameters used for all genes of interest. The section starts with "[gene]" can be used to override default parameters and those specified in the "[general]" section for that gene.
• example command option files framebot_options.txt and 16s_options.txt. The command option file should contain the following information in order, one item per line:gene_name, basedir, workdir, user_email, status_file, result_tar and mail_file.
• an example command file framebot_commands.txt, framebot_cluster_commands.txt. The command file lists the command to be executed in order. Each line contains a tab-separated list containing a command name and the parameters used for that command. See the complete list of commands in fgp_wrapper.py.

Getting Started

• Download the RDPTools and Fungene Pipeline scripts into your local directory.
• Make the directory output_dir. This directory should be empty before you start the script.
• Make an options file. You can use one of the example files as a template; just make sure to adjust the paths accordingly. The file should be in the following format

gene_name  
/path/to/output_dir/basedir  
/path/to/output_dir/workdir  
user_email  
/path/to/output_dir/status_file  
/path/to/output_dir/result_tar  
/path/to/output_dir/mail_file  

• Make a command file. There are several command files in the examplefiles directory to use as templates. Once you are familiar with the pipeline workflow, you can start making your own command files.
• Run the Fungene Pipeline using the following format.
  python /path/to/fungene_pipeline/fgp_wrapper.py options_file.txt command_file.txt input_file

If you are using multiple input files, you can separate them by commas or use *.ext to use all files with the same extension. All of the results will be in the output_dir folder.

Pipeline with command and options file

• Here is an example command to run Initial Process, Chimera Check, Alignment and Clustering using fgp_wrapper.py. Modify the file 16S_options.txt with the correct path to the output directory on your local machine and your email address before run the command:

  /path/to/fungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/16S_options.txt /path/to/fungene_pipeline/examplefiles/init_cluster_commands.txt  
  /path/to/fungene_pipeline/examplefiles/1.TCA.454Reads.fastq  

• An example command to run FrameBot using fgp_wrapper.py. Modify the file framebot_options.txt with the correct path to the output directory on your local machine and your email address before run the command:

  /path/to/fungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/framebot_options.txt /path/to/fungene_pipeline/examplefiles/framebot_commands.txt  
  /path/to/fungene_pipeline/examplefiles/nifH_s1.fa  /path/to/fungene_pipeline/examplefiles/nifH_s2.fa  

• An example command that runs Chimera Check, FrameBot, and Clustering using fgp_wrapper.py.

  /path/tofungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/framebot_options.txt /path/to/fungene_pipeline/examplefiles/framebot_cluster_commands.txt  
  /path/to/fungene_pipeline/examplefiles/nifH_s1.fa /path/to/fungene_pipeline/examplefiles/nifH_s2.fa  

• An example command that runs ChimeraCheck using fgp_wrapper.py.

  /path/tofungene_pipeline/fgp_wrapper.py /path/to/fungene_pipeline/examplefiles/chimeracheck_option.txt /path/to/fungene_pipeline/examplefiles/chimeracheck_command.txt  
  /path/to/fungene_pipeline/examplefiles/1.TCA.454Reads.fna  

Interactive Python

What's include in the Package

• config_skel.ini
  Configuration file containing path of the program and resource files.
• resources
  Contains the alignment models and reference database for each gene
• fgp_wrapper.py
  Runs commands listed in a command file for one input sequence file.
• parseErrorAnalysis.py
  Generates summary output file for the Defined Community Analysis tool.
• pipeline.py
  Takes one sequence file (and optional quality file), runs the following commands in order, Initial Process, Chimera Check, Defined Community Analysis (mock control sample only), FrameBot (protein reads only), Alignment, Clustering, Diversity Analysis(Shanno and Chao), Rarefaction.
• pipeline_core.py
  Contains a set of basic functions to run each individual commands called by other python scripts
• pipeline_wrapper.sh
  A shell script wrapper that runs fgp_wrapper.py
• seq_trimmer_model.py
  Slices a set of alignment sequences.
• titanium_options.py
  Parses a gene option file. Used by other scripts.
• titanium_run_processor.py
  Takes a directory of sequence data files and a run descriptor file. Runs Initial Process and a listed of commands called by pipeline.py.
• examplefiles
  Contains the sample data files and example command and option files used by the Usage example.